problem installing ucsc-bedgraphtobigwig

Question

[gallicchiolorenzo]

Hi,

I am trying to install ucsc-bedgraphtobigwig using the command

conda install -y ucsc-bedgraphtobigwig

However, the process is taking a lot of time and I am receiving these kind of messages:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
Examining conflict for openpyxl et_xmlfile agate-excel: : 301it [38:25,  1.78it/Examining conflict for perl-business-isbn-data perl-uri perl-business-isbn: : 30Examining conflict for perl-business-isbn-data perl-uri perl-business-isbn: : 30Examining conflict for r-ggplot2 r-scales bioconductor-deseq2: : 303it [38:25,  Examining conflict for r-ggplot2 bioconductor-geneplotter r-scales bioconductor-Examining conflict for r-ggplot2 bioconductor-geneplotter r-scales bioconductor-Examining conflict for r-ggplot2 r-viridislite r-scales bioconductor-deseq2: : 3Examining conflict for r-ggplot2 r-viridislite r-scales bioconductor-deseq2: : 3Examining conflict for r-labeling r-ggplot2 r-scales: : 306it [38:31,  1.23it/s]Examining conflict for bioconductor-biocparallel bioconductor-delayedarray biocoExamining conflict for bioconductor-biocparallel bioconductor-delayedarray biocoExamining conflict for bioconductor-biocparallel bioconductor-delayedarray r-futExamining conflict for bioconductor-biocparallel bioconductor-delayedarray r-futExamining conflict for bioconductor-biocparallel bioconductor-delayedarray r-snoExamining conflict for bioconductor-biocparallel bioconductor-delayedarray r-snoExamining conflict for bioconductor-biocparallel r-futile.options r-futile.loggeExamining conflict for bioconductor-biocparallel r-futile.options r-futile.loggeExamining conflict for bioconductor-biocparallel r-futile.logger r-lambda.r: : 3Examining conflict for bioconductor-biocparallel r-futile.logger r-lambda.r: : 3Examining conflict for r-futile.logger r-formatr r-lambda.r: : 314it [38:40,  1.Examining conflict for r-futile.logger r-formatr r-lambda.r: : 315it [38:40,  1.Examining conflict for csvkit agate-excel: : 315it [38:40,  1.05s/it]           Examining conflict for blast perl-exporter-tiny perl-list-moreutils: : 317it [38Examining conflict for blast perl-exporter-tiny perl-list-moreutils: : 318it [38Examining conflict for blast perl-list-moreutils perl-list-moreutils-xs: : 318itExamining conflict for blast perl-list-moreutils perl-list-moreutils-xs: : 319itExamining conflict for blast perl-list-moreutils: : 319it [38:41,  2.46it/s]    Examining conflict for r-ggplot2 r-isoband bioconductor-deseq2: : 320it [38:41, Examining conflict for openpyxl agate-excel: : 321it [38:43,  3.11it/s]         Examining conflict for r-ggplot2 r-mass bioconductor-deseq2: : 324it [38:46,  1.Examining conflict for r-ggplot2 r-mass bioconductor-deseq2: : 325it [38:46,  1.Examining conflict for r-ggplot2 r-mgcv bioconductor-deseq2: : 325it [38:47,  1.Examining conflict for r-ggplot2 r-mgcv bioconductor-deseq2: : 326it [38:47,  1.Examining conflict for bioconductor-geneplotter bioconductor-deseq2: : 326it [38Examining conflict for bioconductor-geneplotter bioconductor-deseq2: : 327it [38Examining conflict for r-callr bioconductor-deseq2: : 327it [38:51,  1.23s/it]  Examining conflict for r-rcpparmadillo bioconductor-deseq2: : 328it [38:52,  1.3Examining conflict for r-rcpparmadillo bioconductor-deseq2: : 329it [38:52,  1.3Examining conflict for clang clangxx: : 329it [38:54,  1.39s/it]             failed                                                             

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - agate -> python=3.4
  - agate-excel -> python[version='2.7.*|3.5.*|3.6.*|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0']
  - blast -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
  - csvkit -> python=3.4
  - leather -> python=3.4
  - picard -> python[version='2.7.*|3.5.*|3.6.*|3.4.*']
  - text-unidecode -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0']

Your python: python=3.8

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (ca-certificates):

  - ucsc-bedgraphtobigwig -> mysql-connector-c[version='>=6.1.11,<6.1.12.0a0'] -> openssl[version='>=1.1.1a,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1d,<1.1.2a']
  - ucsc-bedgraphtobigwig -> openssl[version='>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1g,<1.1.2a']
  - ucsc-bedgraphtobigwig -> openssl[version='>=1.1.1g,<1.1.2a'] -> ca-certificates

The following specifications were found to be incompatible with each other:

And then a huge list XD

I feel the problem might be the Python version I have?

Thanks for the help :)

[gallicchiolorenzo]

Thanks, both solution worked.

Answer 1

[ATpoint]

Create a new environment with conda create -n your_env_name and then install into it. Try to split projects over environments rather than installing everything into the base environment, that at somepoint will make it an unsolvable mess.

Edit: "Unsolvable" => Each time you install a new software conda needs to check that it a) pulls all dependencies for that software with the required versions while b) do not break software that already exists in that environment, e.g. by changing dependency versions. Hence, if you install a lot of stuff into a single environment the solving process takes longer with a growing tree of software and its dependencies, and at some point there might be conflicts that cannot be solved. Like tool-A needs libraryX-version1 and tool-B needs libraryX-version2. That would then be that "unsolvable mess" I wrote above. Therefore it is often better to split over environments

[dariober]

(+1) In addition to that, have a requirements.txt file where you list the programs and their versions. When you need a new program, add it to requirements.txt and then do mamba install --file requirements.txt (I also add --freeze-installed).

Answer 2

[Istvan Albert]

Every once in a while do a:

 conda update --all

or better yet (much faster) you do have mamba right?

 mamba update --all

to upgrade all packages. This often clears up the conflicts when installing new packages.

Alternatively there is another easy way to install the tool. Go to

• http://hgdownload.soe.ucsc.edu/admin/exe/

select your platform and download the executable.